Coral distance conditions

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
Post Reply
Message
Author
Nikos
Member
Posts: 3
Joined: 2017.07.12 12:55

Coral distance conditions

#1 Post by Nikos » 2017.08.18 12:48

Hi,
I am using Coral Version 1.1 (r7883) for linux

When I am defining a distance between two domains as:
dist 21
1 211 211 2 242 242

then the software reads
Condition # 1: Distance 21.000
Between chain # 1, Residues from GLY 211 to GLY 211
and chain # 1, Residues from GLY 566 to GLY 566

My questions:
1. These are not GLY residues, after I test the model it kept the distances as I had defined them with the correct aminoacids (in the sequence 211=SER, 242=566=LEU). Can it read at least the correct aminoacid name?
2. I understand that the numbering is continuous starting from 1, I guess it is also skips any gaps in the sequence. Is that correct?
3. Unfortunately I have more conditions than one (above). I am trying to link some MS crosslinks, so it will be more difficult if I have 4-5 distance restrains between different domains. Any suggestion how to overcome this problem

thanks
Nikos

SaxsMax
Administrator
Posts: 342
Joined: 2007.08.03 19:16

Re: Coral distance conditions

#2 Post by SaxsMax » 2017.08.23 13:08

Please note just in case that in the Coral contact conditions
one should refer to the chain number, not domain number.

Further, the current Coral version concatenates all the chains into one master chain and uses
GLY as DR name identifier. The clarity of the output should be improved in the future releases.

If an input PDB file contains gaps, the corresponding pieces are indeed ignored.

Post Reply